Question: GEOquery error in downloading SOFT files
gravatar for hzc363
14 months ago by
hzc36320 wrote:

I try to download the soft file of a GSM from GEO:


I get the following error:

Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : 
  cannot open URL ''


I then tried to see if it is an internet problem, so I copied the url in the error message and did this:



This time it works. The content in the url is downloaded without problem. 

So my question is, why the getGEO function give me the error and how can I fix it?

I am using "R version 3.3.1 (2016-06-21)" and GEOquery 2.40.0

ADD COMMENTlink modified 14 months ago • written 14 months ago by hzc36320
gravatar for Sean Davis
14 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

An upgrade to GEOquery 2.40 will likely fix the problem.  NCBI has moved away from using "http" in favor of "https", so you'll need to update GEOquery to address that issue.  Sorry for the inconvenience!


ADD COMMENTlink written 14 months ago by Sean Davis21k

upgrade works! Thanks. 

ADD REPLYlink written 14 months ago by hzc36320
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 220 users visited in the last hour